Molecular Modeling Database at NCBI
Tutorial and training materials by OpenHelix
|Learn to use Molecular Modeling Database, or MMDB , which is Entrez's structural database brought to you by the National Institutes of Health and the National Center for Biotechnology Information. It contains an extensive collection of three-dimensional structures with detailed annotation that can be used to learn about the structure and function of many proteins. MMDB's structures were originally obtained from PBD and they contain descriptions, references and extensive multi-directional links both inside and outside of the NCBI network. There are pre-computed structural homologs, i.e. related structures or neighbors, that you can access, and extensive visualization and comparative analysis tools that you can use to examine individual structures, or multiple structures aligned.|
- to search MMDB using both basic and advanced query techniques
- how to understand the detailed results you obtain
- methods to visualize and manipulate structures using NCBI’s Cn3D structural viewer
- to locate and view structurally aligned homologs
Recent BioMed Central research articles citing this resource
Hammesfahr Björn et al., GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures Sequence analysis (applications). BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-77
Mrozek Dariusz et al., search GenBank : interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information Knowledge-based analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-73
Kim Sunghwan et al., PubChem3D: conformer ensemble accuracy. Journal of Cheminformatics (2013) doi:10.1186/1758-2946-5-1
Qiu Wei et al., Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding. BMC Structural Biology (2012) doi:10.1186/1472-6807-12-2
Sousounis Konstantinos et al., Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Human Genomics (2012) doi:10.1186/1479-7364-6-10
More about the resource:
MMDB contains about 40,000 structures with detailed annotation for each. The database can be queried using basic and advanced searching techniques. Each structure has a structure summary page which presents references, ligands present, identifiers, structural homologs and graphical displays. There are many links both within and outside of NCBI's Entrez network of databases on these pages which allow you to find relevant information regarding domains, ligands, homologs, taxonomy and both protein and nucleotide sequences. You can download NCBI’s structural viewer, Cn3D, for visualization and manipulation of the structures and you can also access the database of pre-computed structural homologs to align with your structures.
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